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Computational Systems Biology Projects Tapped for DOE s First Genomes to Life Grants


The US Department of Energy is putting its money — $103 million of it, at least — on computational systems biology.

Last week, the DOE awarded the first grants in its 10-year Genomes to Life initiative to five projects involving 24 different research organizations. To varying degrees, each of the five projects addresses the computational infrastructure that will power the initiative, which aims to characterize molecular and cellular systems of interest for energy production and environmental cleanup.

In a special ceremony last week in Washington, Secretary of Energy Spencer Abraham presented the principal investigators of each of the five projects with ceremonial checks. Adam Arkin from Lawrence Berkeley National Lab, Michelle Buchanan from Oak Ridge National Lab, George Church of Harvard University, Grant Heffelfinger of Sandia National Lab, and Derek Lovely of the University of Massachusetts will head up the five projects.

While all five aim to develop computational systems to elucidate and model the intricacies of cellular systems, the Sandia project has the greatest computational focus, according to Heffelfinger. “Most of the other proposals that were funded have a large element of biology and some computational science. Ours is just the reverse,” he said. And the goals of the Sandia project are ambitious: Heffelfinger and his team plan to tackle everything from data visualization, data reduction, and refinement methods for microarray data all the way to computational infrastructure and high-end operational systems issues.

The specific goals of the Sandia project are related to studying carbon sequestration in the marine bacterium Synechococcus. Heffelfinger said that “significant computational capabilities” need to be developed to marry high-throughput experimental data with structure-property relationships derived from experimental and computational molecular biophysics investigations. The partners will also address the computational challenges of constructing and evaluating cellular models as a collaborative effort.

The project will reconcile a hot debate in the systems biology community — whether it’s better to use a “bottom-up” data-driven approach or a “top-down” reductionist approach to model systems — with a combination of the two methodologies, Heffelfinger said. The goal, he explained, is to develop new simulation methods that are consistent with high-throughput data, yet can be prototyped on real-world biological cellular response problems.

Damien Gessler, principal investigator for the NCGR and a collaborator on the project, explained that the simulations would couple gene and protein sequence data with population dynamics and evolution data in order to derive models of the carbon fixing cycle in Synechococcus populations. “We can model the DNA and sequences of proteins inside cells, then model the cells inside a population, and allow the population to grow and reproduce,” he said. Carbon fixing data can then be “reabstracted” from the simulations.

But cutting-edge simulation work is only part of the Sandia project. Heffelfinger said the researchers also plan to develop a suite of software tools that will allow commodity compute clusters “to seamlessly access large amounts of data.” Oak Ridge National Lab will contribute aspects of its GIST (genome integrated supercomputing toolkit) to the effort.

The project will take at least six months to set up, with initial proposals for models trickling in during the second half of the year, Heffelfinger said.

The awards granted last week were only the first in the 10-year Genomes to Life project, which may have twice as much money to work with next year, according to David Thomassen, program coordinator for the DOE’s office of biological and environmental research. Budget proposals for FY 2003 are still on the table, but Thomassen is confident that Genomes to Life funding will continue to increase. He noted that despite the lack of commercial awards in this year’s batch — Diversa of San Diego was the only commercial recipient — proposals from the private sector are “strongly encouraged.”

“This is the future of biology,” he said. “The payoffs are going to be in both the public and the private sector.”

— BT

Complete List of FY 2002 DOE Genomes to Life Award Recipients

Oak Ridge National Laboratory: $23.4 million over 3 years

Project: Genomes to Life Center for Molecular and Cellular Systems: A Research Program for Identification and Characterization of Protein Complexes

Partners: Pacific Northwest National Lab; Argonne National Lab; Sandia National Lab; University of North Carolina at Chapel Hill, University of Utah


Lawrence Berkeley National Laboratory: $36.6 million over 5 years

Project: Rapid Deduction of Stress Response Pathways in Metal/Radionuclide Reducing Bacteria

Partners: Sandia; Oak Ridge National Lab, University of California at Berkeley; University of Missouri, Columbia; University of Washington, Seattle; Diversa


Sandia National Laboratory: $19.1 million over 3 years

Project: Carbon Sequestration in Synechococcus: From Molecular Machines to Hierarchical Modeling

Partners: Oak Ridge National Lab; Lawrence Berkeley National Lab; Los Alamos National Laboratory; National Center for Genome Resources; University of California at San Diego; University of Tennessee at Knoxville; University of Michigan, Ann Arbor; The Molecular Science Institute; University of California at Santa Barbara; University of Illinois, Champaign.


University of Massachusetts, Amherst: $8.9 million over 3 years

Project: Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the in situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter

Partners: The Institute for Genomic Research; Argonne National Laboratory; University of Tennessee, Memphis.


Harvard Medical School: $15 million over 5 years

Project: Microbial Ecology, Proteogenomics, and Computational Optima

Partners: Massachusetts Institute of Technology; Brigham and Women’s Hospital; Massachusetts General Hospital

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